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16EAGLE16EAGLE
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Updated to include upstream changes as of commit opendatacube/cube-in-a-box@a34c50e 
1 parent 7cd1c99 commit 4211d4f

6 files changed

+185
-50
lines changed

‎Dockerfile

+45-42
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@@ -1,27 +1,31 @@
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FROM ubuntu:focal
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FROM opendatacube/geobase:wheels-3.0.4 as env_builder
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ARG py_env_path=/env
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FROM osgeo/gdal:ubuntu-small-3.3.1
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ENV DEBIAN_FRONTEND=noninteractive \
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LC_ALL=C.UTF-8 \
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LANG=C.UTF-8 \
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TINI_VERSION=v0.19.0 \
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TZ=UTC \
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RPY2_CFFI_MODE=ABI
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# set rpy2 to ABI mode, since R is installed after rpy2
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ENV RPY2_CFFI_MODE=ABI
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# install required python libraries
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RUN mkdir -p /conf
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RUN pip3 install --upgrade pip
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COPY requirements.txt /conf/
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RUN env-build-tool new /conf/requirements.txt ${py_env_path} /wheels
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# install ODC
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FROM opendatacube/geobase:runner-3.0.4
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ARG py_env_path=/env
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ADD https://github.com/krallin/tini/releases/download/${TINI_VERSION}/tini /tini
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RUN chmod +x /tini
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RUN apt-get update && \
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apt-get install -y \
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build-essential \
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git \
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# For Psycopg2
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libpq-dev python3-dev \
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python3-pip \
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wget \
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&& apt-get autoclean \
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&& apt-get autoremove \
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&& rm -rf /var/lib/{apt,dpkg,cache,log}
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COPY --chown=1000:100 --from=env_builder $py_env_path $py_env_path
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COPY --from=env_builder /bin/tini /bin/tini
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RUN export GDAL_DATA=$(gdal-config --datadir)
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ENV LC_ALL=C.UTF-8 \
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PATH="/env/bin:$PATH"
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COPY requirements.txt /conf/
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#COPY products.csv /conf/
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RUN pip3 install --no-cache-dir --requirement /conf/requirements.txt
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RUN useradd -m -s /bin/bash -N jovyan -g 100 -u 1000 \
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&& chown jovyan /home/jovyan \
@@ -46,35 +50,34 @@ RUN echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen \
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&& locale-gen en_US.utf8 \
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&& /usr/sbin/update-locale LANG=en_US.UTF-8
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# set env variables for noninteractive
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ENV LC_ALL en_US.UTF-8
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ENV LANG en_US.UTF-8
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ENV TZ UTC
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# install R and littler, and create a link for littler in /usr/local/bin
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# Default CRAN repo is now set by R itself, and littler knows about it too
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# r-cran-docopt is not currently in c2d4u so we install from source
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ARG DEBIAN_FRONTEND=noninteractive
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RUN apt-get update \
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&& apt-get install -y --no-install-recommends \
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littler \
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r-base \
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r-base-dev \
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r-recommended \
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&& ln -s /usr/lib/R/site-library/littler/examples/install.r /usr/local/bin/install.r \
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&& ln -s /usr/lib/R/site-library/littler/examples/install2.r /usr/local/bin/install2.r \
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&& ln -s /usr/lib/R/site-library/littler/examples/installGithub.r /usr/local/bin/installGithub.r \
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&& ln -s /usr/lib/R/site-library/littler/examples/testInstalled.r /usr/local/bin/testInstalled.r \
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&& install.r docopt \
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&& rm -rf /tmp/downloaded_packages/ /tmp/*.rds \
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&& rm -rf /var/lib/apt/lists/*
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r-base \
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r-base-dev \
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r-recommended \
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&& ln -s /usr/lib/R/site-library/littler/examples/install.r /usr/local/bin/install.r \
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&& ln -s /usr/lib/R/site-library/littler/examples/install2.r /usr/local/bin/install2.r \
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&& ln -s /usr/lib/R/site-library/littler/examples/installGithub.r /usr/local/bin/installGithub.r \
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&& ln -s /usr/lib/R/site-library/littler/examples/testInstalled.r /usr/local/bin/testInstalled.r \
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&& install.r docopt \
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&& rm -rf /tmp/downloaded_packages/ /tmp/*.rds \
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&& rm -rf /var/lib/apt/lists/*
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# install system dependencies for suite of spatial R packages
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ARG DEBIAN_FRONTEND=noninteractive
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RUN apt-get update&&apt-get install -y apt-utils pkg-config
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RUN apt-get install -y libsqlite3-dev libudunits2-dev libssl-dev libmagick++-dev libcurl4-openssl-dev \
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libprotobuf-dev protobuf-compiler libv8-dev libjq-dev
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RUN apt-get update&&apt-get install -y --no-install-recommends r-cran-reticulate
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RUN add-apt-repository --yes "ppa:ubuntugis/ppa" \
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&& apt-get update \
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&& apt-get install -y apt-utils pkg-config \
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&& apt-get install -y libsqlite3-dev libssl-dev \
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libmagick++-dev libcurl4-openssl-dev \
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libprotobuf-dev protobuf-compiler libv8-dev libjq-dev \
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libudunits2-dev libgdal-dev libgeos-dev libproj-dev \
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&& apt-get install -y --no-install-recommends r-cran-reticulate
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# install R packages
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RUN R -e 'install.packages(c("IRkernel", "rgdal", "sp", "raster", "sf", "basemaps", "ggplot2", "mapview", "mapedit", "devtools", "usethis", "testthat", "roxygen2", "geojsonio", "gdalUtils"))'
@@ -94,6 +97,6 @@ WORKDIR /notebooks
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#CMD bash -c " && rstudio-server start"
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#RUN "/init"
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ENTRYPOINT ["/bin/tini", "--"] # "entrypoint.sh"
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CMD ["jupyter", "notebook", "--allow-root", "--ip='0.0.0.0'" "--NotebookApp.token='secretpassword'"]
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ENTRYPOINT ["/tini", "--"]
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CMD ["jupyter", "notebook", "--allow-root", "--ip='0.0.0.0'", "--NotebookApp.token='secretpassword'"]
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#CMD ["rstudio-server start"]

‎Dockerfile.old

+99
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@@ -0,0 +1,99 @@
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FROM ubuntu:focal
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FROM opendatacube/geobase:wheels-3.0.4 as env_builder
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ARG py_env_path=/env
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# set rpy2 to ABI mode, since R is installed after rpy2
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ENV RPY2_CFFI_MODE=ABI
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# install required python libraries
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RUN mkdir -p /conf
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RUN pip3 install --upgrade pip
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COPY requirements.txt /conf/
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RUN env-build-tool new /conf/requirements.txt ${py_env_path} /wheels
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# install ODC
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FROM opendatacube/geobase:runner-3.0.4
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ARG py_env_path=/env
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COPY --chown=1000:100 --from=env_builder $py_env_path $py_env_path
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COPY --from=env_builder /bin/tini /bin/tini
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RUN export GDAL_DATA=$(gdal-config --datadir)
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ENV LC_ALL=C.UTF-8 \
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PATH="/env/bin:$PATH"
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RUN useradd -m -s /bin/bash -N jovyan -g 100 -u 1000 \
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&& chown jovyan /home/jovyan \
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&& addgroup jovyan staff
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# install R dependencies
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RUN apt-get update \
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&& apt-get install -y --no-install-recommends \
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software-properties-common \
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dirmngr \
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ed \
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less \
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locales \
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vim-tiny \
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wget \
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ca-certificates \
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&& add-apt-repository --enable-source --yes "ppa:marutter/rrutter4.0" \
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&& add-apt-repository --enable-source --yes "ppa:c2d4u.team/c2d4u4.0+"
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# configure default locale, see https://github.com/rocker-org/rocker/issues/19
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RUN echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen \
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&& locale-gen en_US.utf8 \
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&& /usr/sbin/update-locale LANG=en_US.UTF-8
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# set env variables for noninteractive
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ENV LC_ALL en_US.UTF-8
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ENV LANG en_US.UTF-8
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ENV TZ UTC
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# install R and littler, and create a link for littler in /usr/local/bin
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# Default CRAN repo is now set by R itself, and littler knows about it too
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# r-cran-docopt is not currently in c2d4u so we install from source
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ARG DEBIAN_FRONTEND=noninteractive
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RUN apt-get update \
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&& apt-get install -y --no-install-recommends \
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littler \
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r-base \
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r-base-dev \
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r-recommended \
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&& ln -s /usr/lib/R/site-library/littler/examples/install.r /usr/local/bin/install.r \
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&& ln -s /usr/lib/R/site-library/littler/examples/install2.r /usr/local/bin/install2.r \
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&& ln -s /usr/lib/R/site-library/littler/examples/installGithub.r /usr/local/bin/installGithub.r \
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&& ln -s /usr/lib/R/site-library/littler/examples/testInstalled.r /usr/local/bin/testInstalled.r \
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&& install.r docopt \
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&& rm -rf /tmp/downloaded_packages/ /tmp/*.rds \
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&& rm -rf /var/lib/apt/lists/*
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# install system dependencies for suite of spatial R packages
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ARG DEBIAN_FRONTEND=noninteractive
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RUN apt-get update&&apt-get install -y apt-utils pkg-config
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RUN apt-get install -y libsqlite3-dev libudunits2-dev libssl-dev libmagick++-dev libcurl4-openssl-dev \
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libprotobuf-dev protobuf-compiler libv8-dev libjq-dev
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RUN apt-get update&&apt-get install -y --no-install-recommends r-cran-reticulate
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# install R packages
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RUN R -e 'install.packages(c("IRkernel", "rgdal", "sp", "raster", "sf", "basemaps", "ggplot2", "mapview", "mapedit", "devtools", "usethis", "testthat", "roxygen2", "geojsonio", "gdalUtils"))'
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RUN R -e 'devtools::install_github("eo2cube/odcr")'
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RUN R -e 'install.packages(c("IRkernel"))'
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# initiliaze R kernel for Jupyter
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RUN R -e "IRkernel::installspec(user = FALSE)"
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## automatically link a shared volume for kitematic users
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#VOLUME /home/rstudio/kitematic
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# set user and working dir
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USER jovyan
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WORKDIR /notebooks
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#CMD bash -c " && rstudio-server start"
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#RUN "/init"
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ENTRYPOINT ["/bin/tini", "--"] # "entrypoint.sh"
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CMD ["jupyter", "notebook", "--allow-root", "--ip='0.0.0.0'" "--NotebookApp.token='secretpassword'"]
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#CMD ["rstudio-server start"]

‎README.md

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@@ -25,7 +25,7 @@ Make sure to have [`docker`](https://docs.docker.com/engine/install/ubuntu/#inst
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Clone this repository to a directory of your choice, e.g. using
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```
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git clone https://github.com/16EAGLE/odcbox/
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git clone https://github.com/eo2cube/odcbox/
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```
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and `cd` into its main directory. To start the container (and build it the first time), run:

‎notebooks/r_s2_odc_example.ipynb

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"mimetype": "text/x-r-source",
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"name": "R",
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"pygments_lexer": "r",
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"version": "4.1.0"
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"version": "4.1.2"
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}
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},
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"nbformat": 4,

‎requirements.txt

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odc-apps-dc-tools
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odc-ui
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odc-index
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# Pinned for Alex to index STAC.
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sat-search==0.3.0
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#sat-search==0.3.0
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# Jupyter components.
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gdal
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scipy
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jupyter==1.0.0
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jupyterlab==2.2.6
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ipyleaflet==0.13.0
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jupyterlab==3.2.0
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ipyleaflet==0.14.0
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folium
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pandas==1.0.5
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pandas==1.3.4
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numpy==1.18
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xarray==0.16.0
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matplotlib==3.2.1
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matplotlib==3.4.3
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geopandas
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scikit-image
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tqdm
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click<8.0.0
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python-dateutil==2.7.5
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dataclasses
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rpy2

‎requirements.txt.old

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--extra-index-url https://packages.dea.ga.gov.au/
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aiohttp
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aiobotocore[boto3,awscli]==1.0.7
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pyyaml
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wget
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requests
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datacube
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odc-algo
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odc-aws
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odc-aio
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odc-apps-cloud
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odc-apps-dc-tools
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odc-ui
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odc-index
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# Pinned for Alex to index STAC.
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sat-search==0.3.0
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# Jupyter components.
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gdal
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scipy
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jupyter==1.0.0
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jupyterlab==2.2.6
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ipyleaflet==0.13.0
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folium
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pandas==1.0.5
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xarray==0.16.0
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matplotlib==3.2.1
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geopandas
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scikit-image
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tqdm
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click<8.0.0
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dataclasses
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rpy2

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